Abstract:[Objective] Bacillus licheniformis is the predominant microbe producing Maotai-flavor in high-temperature Daqu which plays important roles in Maotai-flavor liquor making. Learing the machanisms of tolerance to this liquor making environment with hypertonic, acid and ethanol stress would provide an insight into characterisitcs of this liquor making. [Methods] The resistance to hypertonic, acid and ethanol of B. licheniformis CGMCC 3963 which produces Maotai-flavor was measured. the tolerance machanisms were analyzed on comparative transcriptomics level. [Results] The growth of B. licheniformis CGMCC 3963 in 15% KCl, 15% NaCl, pH 4.0 or 6% ethanol concentration was significantly better than that of B. licheniformis ATCC 14580. Comparative transcriptome analysis revealed a series of genes differently expressed in B. licheniformis CGMCC 3963. [Conclusion] Compared with B. licheniformis ATCC 14580, B. licheniformis CGMCC 3963 posessed a stronger tolerance ability and differently expressed a series of genes related to stress tolerance. Differently expressed genes encoding solute transport, potassium channel protein played important roles in imoproving the tolerance to osmotic stress; genes related to class II heat shock proteins, dehydrogenase, oxidative stress and pH homeostasis made significant contributions to the resistance to acid of B. licheniformis CGMCC 3963; class II and class III heat shock genes were important to ethanol tolerance ability of B. licheniformis CGMCC 3963.